Cellular physiology ATP and Biological Energy (Lecture 15) The complexity of metabolism This schematic diagram traces only a few hundred of the thousands of metabolic reactions that occur in a cell. The dots represent molecules, and the lines represent the chemical reactions that transform them. The reactions proceed in stepwise sequences called metabolic pathways, each step catalyzed by a specific enzyme. Metabolism, Energy and Life The chemistry of life is organized into metabolic pathways Metabolism - totality of an organism s chemical processes Property emerging from specific molecular interactions within the cell Concerned with managing cellular resources: material and energy. Metabolic reactions are organized into pathways that are orderly series of enzymatically controlled reactions. Metabolic pathways are generally of two types: Catabolic pathways release energy by breaking down complex molecules to simpler compounds (cellular respiration which degrades glucose to carbon dioxide and water; provides energy for cellular work); Anabolic pathways consume energy to build complicated molecules from simpler ones (photosynthesis which synthesizes glucose from CO2 and H2O; any synthesis of a macromolecule from its monomers). Organisms transform energy Energy is a capacity to do work Kinetic energy energy in the process of doing work (energy of motion). Heat (thermal energy) is kinetic energy expressed in random movement molecules. Potential energy energy that matter possesses because of its location or arrangement. In the earth s gravitational field, an object on a hill or water behind a dam have potential energy. Chemical energy is potential energy stored in molecules because of the arrangement of nuclei and electrons in its atoms
Energy can be transformed from one form to another Kinetic energy of sunlight can be transformed into the potential energy of chemical bonds during photosynthesis. Potential energy in the chemical bonds of gasoline can be transformed into kinetic mechanical energy which pushes the pistons of an engine The energy transformations of life are subject to two laws of thermodynamics Thermodynamics study of energy transformations First Law of Thermodynamics energy can be transferred and transformed, but it cannot be created or destroyed (energy of the universe is constant) Second Law of Thermodynamics every energy transfer or transformation makes the universe more disordered (every process increases the entropy of the universe). Entropy quantitative measure of disorder that is proportional to randomness Closed system collection of matter under study which is isolated from its surroundings Open system system in which energy can be transferred between the system and its surroundings. The entropy of a system may decrease, but the entropy of the system plus its surroundings must always increase. Highly ordered living organisms do not violate the second law because they are open systems. For example, animals: Maintain highly ordered structure at the expense of increased entropy of their surroundings. Take in complex high energy molecules as food and extract chemical energy to create and maintain order. Return to the surroundings simpler low energy molecules (CO2 and water) and heat. An unstable system is rich in free energy. It has a tendency to change spontaneously to a more stable state. (a) In this case, free energy is proportional to the girl's altitude. (b) The free-energy concept also applies on the molecular scale, in this case to the physical movement of molecules known as diffusion. Here, molecules of a particular solute are distributed unequally across a membrane separating two aqueous compartments. This ordered state is unstable; it is rich in free energy. If the solute molecules can cross the membrane, there will be a net movement (diffusion) of the molecules until they are equally concentrated in both compartments. (c) Chemical reactions also involve free energy. The sugar molecule on top is less stable than the simpler molecules below. When catabolic pathways break down
complex organic molecules, a cell can harness the free energy stored in the molecules to perform work. Organisms live at the expense of free energy Free energy: a criterion for spontaneous change - It is the amount of energy that is available to do work. Free energy (G) is related to the system s total energy (H) and its entropy (S) in the following way: G= H TS Where G = Gibbs free energy H = enthalpy of total energy T = temperature in K S = entropy Free energy (G) = Portion of a system s energy available to do work; is the difference between the total energy (enthalpy) and the energy not available for doing work (TS). The maximum amount of usable energy that can be harvested from a particular reaction is the system s free energy change from the initial to the final state. This change in free energy (ΔG) is given by the Gibbs-Helmholtz equation at constant temperature and pressure: ΔG = ΔH TΔS Where: ΔG = change in free energy ΔH = change in total energy (enthalpy) ΔS = change in entropy T = absolute temperature in K ( C+273) Free energy and equilibrium There is a relationship between chemical equilibrium and the free energy change (ΔG) of a reaction: As a reaction approaches equilibrium, the free energy of the system decreases (spontaneous and exergonic reaction). When a reaction is pushed away from equilibrium, the free energy of system increases (non-spontaneous and endergonic reaction). When a reaction reaches equilibrium, ΔG = 0, because there is no net change in the system. Reactions can be classified based upon their free energy changes:
Exergonic reaction a reaction that proceeds with a net loss of free energy. Endergonic reaction an energy-requiring reaction that proceeds with a net gain of free energy; a reaction absorbs free energy from its surroundings. Free energy and metabolism Exergonic reaction Chemical products have less free energy than the reactant molecules. Reaction is energetically downhill. Spontaneous reaction. ΔG is negative. -ΔG is the maximum amount of work the reaction can perform Endergonic reaction Products store more free energy than reactants Reaction is energetically uphill. Non-spontaneous reaction (requires energy input) ΔG is positive. +ΔG is the minimum amount of work required to drive the reaction. If a chemical process is exergonic, the reverse process must be endergonic. For example: For each mole of glucose oxidized in the exergonic process of cellular respiration, 2870 kj are released (ΔG = -2870 kj/mol or -686 kcal/mol). To produce a mole of glucose, the endergonic process of photosynthesis requires an energy input of 2870 kj (ΔG = +2870 kj/mol or +686 kcal/mol). ATP (a) the structure of ATP and (b) the hydrolysis of ATP to yield ADP and inorganic phosphate. In the cell, most hydroxyl groups of phosphates are ionized (--O negative). The Nature of ATP ATP is the immediate source of energy that power cellular work. ATP powers three main kinds of work in a cell: - mechanical work, cilia beating, the contraction of the muscle cells, the movement of the chromosomes during cellular reproduction; - transport work, the pumping of substances across membranes against the direction of spontaneous movement;
- chemical work, the pushing of endergonic (absorbing free energy from the surrounding) reactions that would not occur spontaneously, such as the synthesis of polymers from monomers. Adenosine triphosphate (ATP), the energy currency or coin of the cell, transfers energy from chemical bonds to endergonic (energy absorbing) reactions within the cell. Structurally, ATP consists of the adenine nucleotide ribose sugar, adenine base, and phosphate group, PO4-2) plus two other phosphate groups. Energy is stored in the covalent bonds between phosphates, with the greatest amount of energy (approximately 7 kcal/mole) in the bond between the second and third phosphate groups. This covalent bond is known as a pyrophosphate bond. Energy coupling by phosphate transfer. In this example, ATP hydrolysis is used to drive an endergonic reaction, the conversion of the amino acid glutamic acid (Glu) to another amino acid, glutamine (Glu--NH2). (a) Without the help of ATP, the conversion is nonspontaneous. (b) As it actually occurs in the cell, the synthesis of glutamine is a two-step reaction driven by ATP. The formation of a phosphorylated intermediate couples the two steps. 1. ATP phosphorylates glutamic acid, making the amino acid less stable. 2. Ammonia displaces the phosphate group, forming glutamine. (c) Adding the delta G for the amino acid conversion to the delta G for the ATP hydrolysis gives the free-energy change for the overall reaction. Because the overall process is exergonic (has a negative delta G), it occurs spontaneously. ATP formation We can write the chemical reaction for the formation of ATP as: a) in chemicalese: ADP + Pi + energy ----> ATP b) in English: Adenosine diphosphate + inorganic Phosphate + energy produces Adenosine Triphosphate The chemical formula for the expenditure/release of ATP energy can be written as: a) in chemicalese: ATP ----> ADP + energy + Pi b) in English Adenosine Triphosphate produces Adenosine diphosphate + energy + inorganic Phosphate How to Make ATP Two processes convert ADP into ATP: 1) substrate-level phosphorylation; and 2) chemiosmosis.
Substrate-level phosphorylation occurs in the cytoplasm when an enzyme attaches a third phosphate to the ADP (both ADP and the phosphates are the substrates on which the enzyme acts). ATP regeneration ATP is renewable and can be regenerated by the addition of phosphate to ADP Exorgenic reaction catabolic reaction providing energy for ATP making Enzymes Enzymes are catalytic proteins that change the rate of a reaction without being consumed by the reaction. The initial investment of energy for starting a reaction the energy required to break bonds in the reactant molecules is known as the free energy of activation, or activation energy. An energy profile of a reaction The reactants AB and CD must absorb enough energy from the surroundings to surmount the hill of activation energy (EA) and reach the unstable transition state. The bonds can then break, and as the reaction proceeds, energy is released to the surroundings during the formation of new bonds. This particular graph profiles the energy inputs and outputs of an exergonic reaction, which has a negative DG; the products have less free energy than the reactants. Enzymes lower the barrier of activation energy Without affecting the free-energy change (delta G) for the reaction, an enzyme speeds the reaction by reducing the uphill climb to the transition state. The black curve shows the course of the reaction without an enzyme; the red curve shows the course of the reaction with an enzyme. Enzymes are substrate-specific The reactant an enzyme acts on is referred to as the enzyme s substrate. Catalytic cycle Enzyme and substrate are available Substrate binds to enzyme Substrate is converted to products Products are released Cofactors Cofactors are nonprotein helpers for catalytic activity; they are either bound tightly to the active site or bound loosely and reversibly along with the substrate. Cofactors may be either inorganic (Zn, Fe, Cu) or organic (specifically called a coenzyme). Most vitamins are coenzymes. Inhibitors
(a) A substrate can normally bind to the active site of an enzyme (b) A competitive inhibitor mimics the substrate and competes for the active site (c) A noncompetitive inhibitor binds to the enzyme at a location away from the active site, but alters the conformation of the enzyme so that the active site is no longer fully functional The control of metabolism The molecules that naturally regulate enzyme activity in a cell act like reversible noncompetitive inhibitors by binding to an allosteric site. Cooperativity In an enzyme molecule with multiple subunits, the binding of one substrate molecule to the active site of one subunit causes all the subunits to assume their active conformation, via the mechanism of induced fit. Enzymes localization Each organelle contain certain number of enzymes that carry out specific functions. Some enzymes and enzyme complexes have fixed locations within the cell as structural components of particular membrane. Others are in solution within specific membrane-enclosed eukaryotic organelles. For example, in eukaryotic cells the enzymes for cellular respiration reside within mitochondria. Conclusions 1. ATP powers cellular work by coupling exergonic reactions to endergonic reactions: it drives endergonic reactions by transfer of the phosphate group to specific reactants cells can carry out work; cell respiration (catabolic pathway) drives the regeneration of ATP from ADP. 2. Enzymes speed up metabolic reactions by lowering energy barriers (activation energy EA). 3. Enzymes are substrate-specific. 4. The active site is an enzyme s catalytic center 5. A cell s physical and chemical environment affects enzyme activity. 6. Metabolic control often depends on allosteric regulation 7. The localization of enzymes within a cell helps order metabolism Chapter 8. 141-159